Eating Sugar While on Antibiotics May Harm Your Gut

Imagine finishing a course of antibiotics and discovering that a few extra desserts sped up the collapse of your gut's microbial community. Strange, but the data point in that direction.

Researchers from NYU, City of Hope and Memorial Sloan Kettering tracked 9,419 hospital meals consumed by 173 patients with blood cancers, recording every tray and sampling gut microbes every day. These patients are a revealing cohort: frequent antibiotic use, precisely logged hospital diets and vulnerable immune systems make subtle shifts in the microbiome easier to spot.

What they found was stark. For every additional 100 grams of sugar eaten in the 48 hours before treatment, alpha diversity—the measure of variety among bacterial species in the gut—fell an extra 21 percent. Less variety. Less resilience. A microbiome more prone to being dominated by a few hardy survivors.

One of those survivors was Enterococcus faecium, a bacterium linked to difficult-to-treat infections. Patients who combined higher-sugar diets with antibiotic treatment showed blooms of this species. That pattern matters especially for people undergoing stem cell transplants, who often spend weeks in hospital, endure chemotherapy, and receive repeated antibiotic courses; their gut ecosystems can be dramatically stripped, creating ecological vacancies that opportunists like Enterococcus readily exploit.

Animal tests echoed the human findings. Mice given antibiotics plus sucrose developed dramatic Enterococcus expansions: roughly a 16.3-fold jump by day three and about 33.4-fold by day six. The numbers are hard to ignore.

Exactly how sugar amplifies the effect remains an open question. Does sugar directly fuel surviving Enterococcus cells? Does it weaken competitor species, leaving a clearer path? Or does it alter host responses in ways that favor certain microbes? The scientists emphasize that the mechanism is unresolved and that more clinical research is required.

Limiting simple sugars during and after antibiotic therapy could reduce microbiome damage, though definitive clinical guidance awaits further trials.

The study, published in Nature, adds to a growing picture: diet and drugs interact to shape microbial ecology in consequential ways. So the next time you reach for sweets while on antibiotics, pause—ask your care team whether a different snack might be the safer bet.